/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2020 UniPro <ugene@unipro.ru>
 * http://ugene.net
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
 * MA 02110-1301, USA.
 */

#ifndef __PHYTREEGENERATORTASK_H
#define __PHYTREEGENERATORTASK_H

#include <U2Algorithm/CreatePhyTreeSettings.h>

#include <U2Core/Task.h>

#include "PhyTreeGenerator.h"

namespace U2 {

class U2ALGORITHM_EXPORT PhyTreeGeneratorTask : public Task {
    Q_OBJECT
public:
    PhyTreeGeneratorTask(const MultipleSequenceAlignment &ma, const CreatePhyTreeSettings &_settings);
    ~PhyTreeGeneratorTask() {
    }
    void run();
    PhyTree getResult() {
        return result;
    }
    const CreatePhyTreeSettings &getSettings() {
        return settings;
    }
    ReportResult report();

protected:
    const MultipleSequenceAlignment inputMA;
    PhyTree result;
    CreatePhyTreeSettings settings;
};

class SeqNamesConvertor {
public:
    SeqNamesConvertor()
        : lastIdStr("a") {
    }

    void replaceNamesWithAlphabeticIds(MultipleSequenceAlignment &ma);
    void restoreNames(const PhyTree &tree);

private:
    const QString &generateNewAlphabeticId();

    QString lastIdStr;
    QMap<QString, QString> namesMap;
};

class U2ALGORITHM_EXPORT PhyTreeGeneratorLauncherTask : public Task {
    Q_OBJECT
public:
    PhyTreeGeneratorLauncherTask(const MultipleSequenceAlignment &ma, const CreatePhyTreeSettings &_settings);
    ~PhyTreeGeneratorLauncherTask() {};
    PhyTree getResult() {
        return result;
    }
    void prepare();
    void run() {};
    ReportResult report();
private slots:
    void sl_onCalculationCanceled();

private:
    MultipleSequenceAlignment inputMA;
    PhyTree result;
    CreatePhyTreeSettings settings;
    PhyTreeGeneratorTask *task;
    SeqNamesConvertor namesConvertor;
};

}    // namespace U2

#endif
